In the most aggressive -- and, some say, invasive -- step yet to protect air travelers, the federal government and the airlines will phase in a computer system next year to measure the risk posed by every passenger on every flight in the United States.

The new Transportation Security Administration system seeks to probe deeper into each passenger's identity than is currently possible, comparing personal information against criminal records and intelligence information. Passengers will be assigned a color code -- green, yellow or red -- based in part on their city of departure, destination, traveling companions and date of ticket purchase.

Most people will be coded green and sail through. But up to 8 percent of passengers who board the nation's 26,000 daily flights will be coded "yellow" and will undergo additional screening at the checkpoint, according to people familiar with the program. An estimated 1 to 2 percent will be labeled "red" and will be prohibited from boarding. These passengers also will face police questioning and may be arrested.

The system "will provide protections for the flying public," said TSA spokesman Brian Turmail. "Not only should we keep passengers from sitting next to a terrorist, we should keep them from sitting next to wanted ax murderers."

The new system, called Computer Assisted Passenger Pre-screening System II (CAPPS II), has sparked so much controversy among both liberal and conservative groups that the TSA has struggled to get it going. Delta Air Lines backed out of a testing program with the agency earlier this year, and now the TSA will not reveal which airlines will participate when it tests a prototype early next year. If all goes as planned, the TSA will begin the new computer screening of some passengers as early as next summer and eventually it will be used for all domestic travelers.

"This system is going to be replete with errors," said Barry Steinhardt, director of the American Civil Liberties Union's technology and liberty program. "You could be falsely arrested. You could be delayed. You could lose your ability to travel."

In the two years since the Sept. 11, 2001, terrorist hijackings, air security has taken a high priority, and the government has spent $9 billion on improvements. Thousands of explosives-detection machines now scan checked luggage at airports across the nation. A new force of federal airport screeners staffs checkpoints, though next year some airports may revert to private screeners. Cockpit doors have been reinforced, and hundreds of airline pilots now carry guns. In addition, the force of undercover air marshals has been expanded, and as many as 5,000 federal immigration and customs agents will be trained to bolster the force on a temporary basis when the government perceives a heightened threat.

Still, many holes in security persist. Airports and aircraft still appear easy to penetrate, illustrated last month by an accidental landing of several boaters on the airfield at John F. Kennedy International Airport. Air cargo remains vulnerable, as virtually none of the items stowed alongside luggage in the aircraft hold are screened for explosives. Government officials continue to assess how best to respond to the possibility of a shoulder-fired missile attack at a commercial airliner, which they maintain is a serious threat.

In the coming months, major airports in Los Angeles, Seattle, Denver and Dallas will embark on extensive construction projects to build explosives-detection machines into conveyor-belt systems that sort checked luggage being loaded onto planes. (Other airports, including Washington's, are waiting in line for hundreds of millions of dollars in government funding.)

Clearly, the TSA says, the job of protecting the nation's skies is not done.

"Given the dynamic nature of the threat we deal with, it would be impossible to predict when the work would be finished" on air security, said TSA spokesman Robert Johnson. "We don't think it will ever end."

The government says the most significant change in security is still to come in the form of CAPPS II. The current computer screener program was developed by U.S. airlines in the mid-1990s in response to government and public pressure to improve air security after terrorists blew up Pan Am Flight 103 over Lockerbie, Scotland.

The existing system identifies certain passengers as risky based on a set of assumptions about how terrorists travel. For instance, passengers are flagged for additional screening if they bought a one-way airline ticket, or if they paid with cash instead of a credit card. Passengers who present a threat under these and other criteria are issued boarding passes that bear a coding of "SSS" or "***."

But the TSA, recognizing that the system is outdated and easy to fool, wants to replace it and put the government in the role now played by the airlines in making security assessments.

Under the new program, the airline will send information about everyone who books a flight to the TSA, including full name, home address, home telephone number, date of birth and travel itinerary. If the computer system identifies a threat, the TSA will notify federal or local law enforcement authorities. The agency has not indicated the number or type of personnel needed to oversee the program.

The TSA will check each passenger in two steps. The first will match the passenger's name and information against databases of private companies that collect information on people for commercial reasons, such as their shopping habits. This process will generate a numerical score that will indicate the likelihood that the passenger is who he says he is. Passengers will not be informed of their color code or their numerical score. The second step matches passenger information against government intelligence combined with local and state outstanding warrants for violent felonies.

Airlines like the system because they think it will reduce time passengers spend at security checkpoints and lower the likelihood that they will be delayed for their flights. The TSA said the program is expected to flag fewer people than the current computer screening system. The agency intends to test the program in several phases to ensure that it works as promised.

"If it delivers the way it's envisioned, it's going to be a significant, positive change," the TSA's Johnson said. "It's going to be a lot fewer people [flagged], but we think it will be the right people."

David A. Keene, chairman of the American Conservative Union, worries that the computer screening program will go beyond its original goals. "This system is not designed just to get potential terrorists," Keene said. "It's a law enforcement tool. The wider the net you cast, the more people you bring in."

As the government takes a new, large role in one aspect of screening, it is rolling back its presence in another. By late 2004, some airports are expected to replace the federal screening force with private screeners. A security law passed after the terrorist attacks allows airports to "opt out" of the government's federal screening workforce in November 2004. Many airports, frustrated with the staffing cuts and the inability to control the number of screeners at each station, believe they might have more control over the operations if a private company were in charge.

"I've been in various meetings with many airport managers who are saying, 'We don't want as much government control around,' " said James McNeil, chief executive of McNeil Technologies Inc., which provides security screeners at the airport in Rochester, N.Y., one of five test airports that employ private screeners. McNeil said he has talked to 20 to 30 airports that are interested in his services. A large association of the nation's airports estimates that many small airports will opt out of government screeners next year because their limited flight schedules require that screeners work flexible hours. The government will still have a role in security because the private screening companies will operate under contracts managed by the TSA.

If many airports, particularly large hubs that handle a major portion of the nation's 30,000 daily flights, choose to revert to the private screening force, some aviation industry leaders have wondered what that will mean for the TSA.

The agency, created just months after the terrorist attacks, has already seen some of its authority stripped. The Federal Air Marshal Service has moved to a law enforcement division within the Department of Homeland Security, as has the agency's explosives unit. Some of its security directors claim they are still out of the loop on some of the agency's latest intelligence on air security.

Johnson, the TSA spokesman, hinted that the agency's future is unclear.

"We've got a department-level organization now created for that sole purpose [of fighting terrorism] and it only makes sense, where necessary, to economize and coordinate," Johnson said. "There will always be a need to provide the best aviation security possible at airports. Whether it's under one flag or another, it really makes no difference."

 Tom Ridge, Secretary of Homeland Security Robert G. Kaiser, Post associate editor, on the nation two years later Keith Alexander, Post business staff writer, on the airline industry Vernon Loeb, Post military reporter, on national security and the military Mel Goodman, analyst and author, on national security

 Noon, Thursday: The Post's Keith Alexander on the state of the airlines -- two years after 9/11.  1 p.m., Thursday: The Post's Ben White will discuss the NYSE pay package and executive compensation.